Doesn't Digital Juice give you the option of codec to render the animations to? Mp4 seems like an odd intermediate codec for files that should have an alpha channel. I could be mistaken, but I don't think alpha channels are supported in standard mp4.
I thought that those animation loops should be exported form The Juicer™ as uncompressed AVI or QT files with an alpha channel for transparency. An uncompressed file will be better for changing the color palette with premiere's fx as well.
Solid colors will be easier to change with proc amp, color replace, fast CC, 3-way CC, tint, color balance RGB, RGB CC, etc.
Adjusting gradients may be more of a change with those tools.
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